Beta diversity analysis of samples of ruminal liquid of 4 animals (collected at the sloather house): I1, I2, I3 and I4. Control group consists in ruminal liquid + diet, treatments consist of control and AE1, AE sintethyc 1, Carvacrol, p-cymene, gamma-terpinene.

Comparison 1) Beta diversity: RUMINAL LIQUID VS CONTROL (RUMINAL LIQUID +DIET)

Between-sample variability from 16S rRna-gene sequencing data.

Clustering

PCA

Clustering by treatment (PCA) - ruminal liquid & control:

MDS

Clustering by treatment (MDS): NMDS1 vs NMDS2

## Warning in metaMDS(matx0, k = 3): stress is (nearly) zero: you may have
## insufficient data

Clustering by type (MDS): NMDS1 vs NMDS3

Clustering by type (MDS): NMDS2 vs NMDS3

Clustering by treatment by timepoint (MDS):

Significance of between-group distances

Significance values based on permuted analysis of variance (999 permutations), repeated 100 times.

  • between treatments: p-value = 0.38205 (std = 0.0146587)

Below the ANOVA table from the model:

\[ X = \mu + treatment + timepoint + treatment*type + e \]

Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
treatment 1 0.0099243 0.0099243 0.8717938 0.0801886 0.381
residuals 10 0.1138372 0.0113837 NA 0.9198114 NA
total 11 0.1237615 NA NA 1.0000000 NA

Going 3D

## Run 0 stress 0.008349506 
## Run 1 stress 0.008361132 
## ... Procrustes: rmse 0.0006056323  max resid 0.001177857 
## ... Similar to previous best
## Run 2 stress 0.009198531 
## Run 3 stress 0.009486074 
## Run 4 stress 0.008528749 
## ... Procrustes: rmse 0.007940972  max resid 0.01444052 
## Run 5 stress 0.009099832 
## Run 6 stress 0.008400782 
## ... Procrustes: rmse 0.002416866  max resid 0.003687478 
## ... Similar to previous best
## Run 7 stress 0.009092253 
## Run 8 stress 0.008305532 
## ... New best solution
## ... Procrustes: rmse 0.004207716  max resid 0.008817356 
## ... Similar to previous best
## Run 9 stress 0.009205873 
## Run 10 stress 0.01937812 
## Run 11 stress 0.01941995 
## Run 12 stress 0.009193597 
## Run 13 stress 0.01960857 
## Run 14 stress 0.01973618 
## Run 15 stress 0.008418068 
## ... Procrustes: rmse 0.005612771  max resid 0.008920026 
## Run 16 stress 0.00919722 
## Run 17 stress 0.009201285 
## Run 18 stress 0.01946978 
## Run 19 stress 0.008314335 
## ... Procrustes: rmse 0.00114829  max resid 0.002707772 
## ... Similar to previous best
## Run 20 stress 0.009197261 
## *** Solution reached

Comparison 2) Beta diversity: CONTROL VS TREATMENTS (control and treatments have all the same base of ruminal liquid+diet)

Between-sample variability from 16S rRna-gene sequencing data.

Clustering

PCA

Clustering by timepoint (PCA), removing ruminal liquid samples (I1 to I4):

Clustering by treatment (PCA)

MDS

Clustering by treatment (MDS): NMDS1 vs NMDS2

Clustering by type (MDS): NMDS1 vs NMDS3

Clustering by type (MDS): NMDS2 vs NMDS3

Clustering by treatment by timepoint (MDS):

Significance of between-group distances

Significance values based on permuted analysis of variance (999 permutations), repeated 100 times.

Between treatments: p-value = 0.95323 (std = 0.0073304)

Below the ANOVA table from the model:

\[ X = \mu + treatment + timepoint + treatment*type + e \]

Df SumsOfSqs MeanSqs F.Model R2 Pr(>F)
treatment 5 0.0433895 0.0086779 0.4765167 0.0536828 0.957
residuals 42 0.7648664 0.0182111 NA 0.9463172 NA
total 47 0.8082558 NA NA 1.0000000 NA

going 3D

## Run 0 stress 0.01298168 
## Run 1 stress 0.01343476 
## ... Procrustes: rmse 0.005814629  max resid 0.03097529 
## Run 2 stress 0.01305155 
## ... Procrustes: rmse 0.001694783  max resid 0.004779158 
## ... Similar to previous best
## Run 3 stress 0.01321474 
## ... Procrustes: rmse 0.004034552  max resid 0.01080194 
## Run 4 stress 0.01298176 
## ... Procrustes: rmse 6.156712e-05  max resid 9.928578e-05 
## ... Similar to previous best
## Run 5 stress 0.01298313 
## ... Procrustes: rmse 0.0003468209  max resid 0.0005708492 
## ... Similar to previous best
## Run 6 stress 0.0137477 
## Run 7 stress 0.01298363 
## ... Procrustes: rmse 0.0003651463  max resid 0.0005339837 
## ... Similar to previous best
## Run 8 stress 0.01299097 
## ... Procrustes: rmse 0.0009828238  max resid 0.001699637 
## ... Similar to previous best
## Run 9 stress 0.01302572 
## ... Procrustes: rmse 0.002387891  max resid 0.004365122 
## ... Similar to previous best
## Run 10 stress 0.01346863 
## ... Procrustes: rmse 0.004861004  max resid 0.01296442 
## Run 11 stress 0.01298465 
## ... Procrustes: rmse 0.0003201583  max resid 0.0005145715 
## ... Similar to previous best
## Run 12 stress 0.01344956 
## ... Procrustes: rmse 0.005961833  max resid 0.02966442 
## Run 13 stress 0.01298693 
## ... Procrustes: rmse 0.0007027888  max resid 0.001185948 
## ... Similar to previous best
## Run 14 stress 0.01345628 
## ... Procrustes: rmse 0.006062346  max resid 0.03015098 
## Run 15 stress 0.01343369 
## ... Procrustes: rmse 0.005813414  max resid 0.03124598 
## Run 16 stress 0.01343993 
## ... Procrustes: rmse 0.005859207  max resid 0.03043586 
## Run 17 stress 0.01299213 
## ... Procrustes: rmse 0.001041224  max resid 0.001821031 
## ... Similar to previous best
## Run 18 stress 0.01298161 
## ... New best solution
## ... Procrustes: rmse 7.462513e-05  max resid 0.0001719395 
## ... Similar to previous best
## Run 19 stress 0.01343873 
## ... Procrustes: rmse 0.005871508  max resid 0.03123103 
## Run 20 stress 0.01298691 
## ... Procrustes: rmse 0.0007380376  max resid 0.001210857 
## ... Similar to previous best
## *** Solution reached

Treatment AE1

timepoint AE sintético 1

treatment Carvacrol

treatment p-cymene

treatment γ-terpinene

treatment Control